Starting phenix.real_space_refine on Thu Mar 6 03:58:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zlo_60231/03_2025/8zlo_60231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zlo_60231/03_2025/8zlo_60231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zlo_60231/03_2025/8zlo_60231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zlo_60231/03_2025/8zlo_60231.map" model { file = "/net/cci-nas-00/data/ceres_data/8zlo_60231/03_2025/8zlo_60231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zlo_60231/03_2025/8zlo_60231.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 10 7.06 5 S 10 5.16 5 C 3030 2.51 5 N 836 2.21 5 O 920 1.98 5 F 10 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4816 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "G" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "I" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "J" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "O" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "T" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'1KI': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'1KI': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.61, per 1000 atoms: 0.75 Number of scatterers: 4816 At special positions: 0 Unit cell: (78.85, 96.28, 49.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 10 34.99 S 10 16.00 F 10 9.00 O 920 8.00 N 836 7.00 C 3030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 598.3 milliseconds 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 48 removed outlier: 6.723A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.423A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR E 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.511A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL E 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.360A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA E 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 93 removed outlier: 8.872A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 91 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR I 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA E 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLY I 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR E 92 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA E 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR J 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA J 91 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR T 92 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.723A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.423A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.512A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.361A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 93 removed outlier: 8.872A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA C 91 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR G 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA F 91 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR H 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA H 91 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR O 92 " --> pdb=" O ALA H 91 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 1582 1.35 - 1.50: 1415 1.50 - 1.65: 1821 1.65 - 1.79: 20 1.79 - 1.94: 10 Bond restraints: 4848 Sorted by residual: bond pdb=" C13 1KI I 101 " pdb=" C14 1KI I 101 " ideal model delta sigma weight residual 1.409 1.297 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C13 1KI G 101 " pdb=" C14 1KI G 101 " ideal model delta sigma weight residual 1.409 1.297 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C12 1KI G 101 " pdb=" C13 1KI G 101 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C12 1KI I 101 " pdb=" C13 1KI I 101 " ideal model delta sigma weight residual 1.390 1.465 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C13 1KI G 103 " pdb=" C14 1KI G 103 " ideal model delta sigma weight residual 1.409 1.340 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 4843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 5855 2.35 - 4.71: 564 4.71 - 7.06: 95 7.06 - 9.42: 16 9.42 - 11.77: 12 Bond angle restraints: 6542 Sorted by residual: angle pdb=" C03 1KI I 101 " pdb=" N04 1KI I 101 " pdb=" C05 1KI I 101 " ideal model delta sigma weight residual 115.28 127.05 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C03 1KI G 101 " pdb=" N04 1KI G 101 " pdb=" C05 1KI G 101 " ideal model delta sigma weight residual 115.28 127.01 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N ILE E 88 " pdb=" CA ILE E 88 " pdb=" C ILE E 88 " ideal model delta sigma weight residual 108.12 103.39 4.73 1.34e+00 5.57e-01 1.24e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 108.12 103.41 4.71 1.34e+00 5.57e-01 1.24e+01 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 108.12 103.42 4.70 1.34e+00 5.57e-01 1.23e+01 ... (remaining 6537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2504 17.68 - 35.37: 185 35.37 - 53.05: 66 53.05 - 70.74: 15 70.74 - 88.42: 18 Dihedral angle restraints: 2788 sinusoidal: 1012 harmonic: 1776 Sorted by residual: dihedral pdb=" CA GLY G 67 " pdb=" C GLY G 67 " pdb=" N GLY G 68 " pdb=" CA GLY G 68 " ideal model delta harmonic sigma weight residual 0.00 25.06 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY O 67 " pdb=" C GLY O 67 " pdb=" N GLY O 68 " pdb=" CA GLY O 68 " ideal model delta harmonic sigma weight residual 0.00 25.05 -25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY D 67 " pdb=" C GLY D 67 " pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta harmonic sigma weight residual 0.00 25.05 -25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 2785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 436 0.052 - 0.104: 202 0.104 - 0.157: 118 0.157 - 0.209: 24 0.209 - 0.261: 24 Chirality restraints: 804 Sorted by residual: chirality pdb=" CA ILE J 88 " pdb=" N ILE J 88 " pdb=" C ILE J 88 " pdb=" CB ILE J 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE H 88 " pdb=" N ILE H 88 " pdb=" C ILE H 88 " pdb=" CB ILE H 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 801 not shown) Planarity restraints: 808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 52 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C VAL D 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL D 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA D 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 52 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C VAL B 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL B 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA B 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 52 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C VAL E 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL E 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 53 " 0.013 2.00e-02 2.50e+03 ... (remaining 805 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 86 2.63 - 3.20: 3873 3.20 - 3.77: 7134 3.77 - 4.33: 9965 4.33 - 4.90: 19076 Nonbonded interactions: 40134 Sorted by model distance: nonbonded pdb=" O GLY D 51 " pdb=" O24 1KI G 103 " model vdw 2.063 3.040 nonbonded pdb=" O GLY B 51 " pdb=" O24 1KI I 103 " model vdw 2.064 3.040 nonbonded pdb=" O GLY G 51 " pdb=" O24 1KI H 101 " model vdw 2.123 3.040 nonbonded pdb=" O GLY I 51 " pdb=" O24 1KI J 101 " model vdw 2.123 3.040 nonbonded pdb=" O GLY A 51 " pdb=" O24 1KI E 101 " model vdw 2.157 3.040 ... (remaining 40129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.112 4848 Z= 0.979 Angle : 1.517 11.774 6542 Z= 0.797 Chirality : 0.081 0.261 804 Planarity : 0.006 0.023 808 Dihedral : 17.146 88.421 1660 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.25), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 50 PHE 0.016 0.008 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.497 Fit side-chains REVERT: F 83 GLU cc_start: 0.6332 (mt-10) cc_final: 0.5759 (mp0) REVERT: H 83 GLU cc_start: 0.5988 (mt-10) cc_final: 0.5785 (mt-10) REVERT: I 72 THR cc_start: 0.7197 (m) cc_final: 0.6914 (p) REVERT: J 83 GLU cc_start: 0.5695 (mt-10) cc_final: 0.5280 (mp0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2146 time to fit residues: 20.3173 Evaluate side-chains 55 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.170799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.120249 restraints weight = 2746.750| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.85 r_work: 0.3671 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4848 Z= 0.414 Angle : 1.091 13.937 6542 Z= 0.499 Chirality : 0.056 0.159 804 Planarity : 0.003 0.015 808 Dihedral : 14.141 92.050 748 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 6.58 % Allowed : 12.72 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.18), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.019 0.004 PHE H 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.451 Fit side-chains REVERT: H 97 LYS cc_start: 0.8248 (mttt) cc_final: 0.7992 (mttm) outliers start: 30 outliers final: 25 residues processed: 78 average time/residue: 0.1885 time to fit residues: 18.4187 Evaluate side-chains 72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 23 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS D 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.161751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.110467 restraints weight = 2653.910| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.77 r_work: 0.3571 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4848 Z= 0.382 Angle : 0.932 12.424 6542 Z= 0.436 Chirality : 0.055 0.158 804 Planarity : 0.003 0.015 808 Dihedral : 11.554 82.761 748 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 8.55 % Allowed : 8.33 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.18), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.013 0.003 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 58 time to evaluate : 0.497 Fit side-chains REVERT: F 79 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8629 (mt0) REVERT: G 97 LYS cc_start: 0.9026 (mttm) cc_final: 0.8792 (mttp) REVERT: H 97 LYS cc_start: 0.8640 (mttt) cc_final: 0.8434 (mttm) REVERT: I 97 LYS cc_start: 0.9024 (mttm) cc_final: 0.8559 (mttp) REVERT: J 79 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: T 98 ASP cc_start: 0.7731 (m-30) cc_final: 0.7383 (m-30) outliers start: 39 outliers final: 28 residues processed: 88 average time/residue: 0.1971 time to fit residues: 21.4612 Evaluate side-chains 80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN O 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.157546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106068 restraints weight = 2748.049| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.82 r_work: 0.3494 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 4848 Z= 0.485 Angle : 0.957 12.836 6542 Z= 0.454 Chirality : 0.057 0.163 804 Planarity : 0.003 0.012 808 Dihedral : 11.262 77.625 748 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 7.46 % Allowed : 9.87 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.24), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 50 PHE 0.016 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.505 Fit side-chains REVERT: B 79 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8613 (mt0) REVERT: F 79 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8691 (mt0) outliers start: 34 outliers final: 29 residues processed: 82 average time/residue: 0.1762 time to fit residues: 18.3586 Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN H 99 GLN J 79 GLN T 79 GLN T 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.162486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111096 restraints weight = 2701.893| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.86 r_work: 0.3592 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4848 Z= 0.196 Angle : 0.737 12.346 6542 Z= 0.331 Chirality : 0.051 0.146 804 Planarity : 0.002 0.013 808 Dihedral : 9.540 72.515 748 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.82 % Allowed : 12.72 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.25), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.008 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.501 Fit side-chains REVERT: O 52 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8264 (t) outliers start: 22 outliers final: 18 residues processed: 79 average time/residue: 0.1901 time to fit residues: 18.8671 Evaluate side-chains 79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN T 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.166222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.115748 restraints weight = 2715.324| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.77 r_work: 0.3602 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.7453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4848 Z= 0.171 Angle : 0.690 11.957 6542 Z= 0.308 Chirality : 0.050 0.145 804 Planarity : 0.002 0.011 808 Dihedral : 8.947 70.772 748 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.82 % Allowed : 11.40 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 50 PHE 0.007 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.520 Fit side-chains REVERT: F 79 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: O 52 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8350 (t) outliers start: 22 outliers final: 19 residues processed: 76 average time/residue: 0.1960 time to fit residues: 18.6627 Evaluate side-chains 81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN T 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.154656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103376 restraints weight = 2797.579| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.83 r_work: 0.3452 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.042 4848 Z= 0.633 Angle : 1.008 13.475 6542 Z= 0.484 Chirality : 0.059 0.169 804 Planarity : 0.003 0.010 808 Dihedral : 11.754 74.972 748 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 5.70 % Allowed : 11.18 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS T 50 PHE 0.016 0.004 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.487 Fit side-chains REVERT: F 79 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8659 (mt0) REVERT: G 99 GLN cc_start: 0.6419 (mt0) cc_final: 0.5848 (mp10) REVERT: I 99 GLN cc_start: 0.6268 (mt0) cc_final: 0.6061 (mt0) outliers start: 26 outliers final: 24 residues processed: 80 average time/residue: 0.1744 time to fit residues: 17.8720 Evaluate side-chains 89 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.159213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.109562 restraints weight = 2778.856| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.77 r_work: 0.3521 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.7964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4848 Z= 0.295 Angle : 0.800 13.052 6542 Z= 0.366 Chirality : 0.052 0.153 804 Planarity : 0.002 0.011 808 Dihedral : 10.544 82.967 748 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.82 % Allowed : 12.06 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.26), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.010 0.002 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.511 Fit side-chains REVERT: F 79 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: G 99 GLN cc_start: 0.6331 (mt0) cc_final: 0.5793 (mp10) REVERT: I 99 GLN cc_start: 0.6083 (mt0) cc_final: 0.5880 (mt0) outliers start: 22 outliers final: 21 residues processed: 78 average time/residue: 0.1830 time to fit residues: 18.3911 Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.0070 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.157718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.108285 restraints weight = 2849.476| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.80 r_work: 0.3560 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4848 Z= 0.213 Angle : 0.727 12.676 6542 Z= 0.328 Chirality : 0.051 0.147 804 Planarity : 0.002 0.010 808 Dihedral : 9.777 81.246 748 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.61 % Allowed : 12.72 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.008 0.002 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.458 Fit side-chains REVERT: F 79 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: G 99 GLN cc_start: 0.6268 (mt0) cc_final: 0.5733 (mp10) REVERT: H 97 LYS cc_start: 0.8710 (mttt) cc_final: 0.8492 (mttm) REVERT: I 99 GLN cc_start: 0.6233 (mt0) cc_final: 0.6031 (mt0) outliers start: 21 outliers final: 20 residues processed: 75 average time/residue: 0.1922 time to fit residues: 18.3461 Evaluate side-chains 84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.155852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.105235 restraints weight = 2823.019| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.84 r_work: 0.3511 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.8105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4848 Z= 0.320 Angle : 0.801 12.893 6542 Z= 0.370 Chirality : 0.052 0.151 804 Planarity : 0.002 0.009 808 Dihedral : 10.086 77.930 748 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.82 % Allowed : 12.50 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.010 0.002 PHE C 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.405 Fit side-chains REVERT: F 79 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: G 99 GLN cc_start: 0.6366 (mt0) cc_final: 0.6088 (mp10) REVERT: I 99 GLN cc_start: 0.6206 (mt0) cc_final: 0.6003 (mt0) REVERT: O 99 GLN cc_start: 0.5598 (tm-30) cc_final: 0.4881 (mt0) outliers start: 22 outliers final: 21 residues processed: 78 average time/residue: 0.2150 time to fit residues: 21.0467 Evaluate side-chains 88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.152774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.102109 restraints weight = 2927.034| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.85 r_work: 0.3458 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.8312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 4848 Z= 0.488 Angle : 0.928 13.324 6542 Z= 0.440 Chirality : 0.056 0.162 804 Planarity : 0.003 0.010 808 Dihedral : 11.180 76.328 748 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 5.70 % Allowed : 11.18 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS T 50 PHE 0.013 0.003 PHE I 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.90 seconds wall clock time: 50 minutes 2.79 seconds (3002.79 seconds total)